


From Superhero to Superagent

by Keener_girl



Category: Marvel Cinematic Universe, Spider-Man: Homecoming (2017)
Genre: F/M, Father-Son Relationship
Language: English
Status: In-Progress
Published: 2019-06-18
Updated: 2019-06-18
Packaged: 2020-05-14 08:21:52
Rating: Teen And Up Audiences
Warnings: Graphic Depictions Of Violence
Chapters: 2
Words: 3,557
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19269391
Author URL: https://archiveofourown.org/users/Keener_girl/pseuds/Keener_girl
Summary: When Tony acts out of his fear of losing Peter once again, he ends up with a wall between him and the teen. Peter stops telling him things, keeps secrets, and refuses to spend any time with the billionaire. Tony is upset, while Peter himself is beyond hurt by the words Tony let slip while vulnerable. However, when Nick Fury shows up and says the words that the teen couldn't help but think should be coming out of Tony's mouth, he easily decides to prove his worth to the seemingly cold-hearted billionaire and help Nick Fury save the world....and hope that Tony doesn't murder him when he discovers what Peter has been doing behind his back.Note: This is set after Endgame, and is a universe that I made up where Tony Stark lives.





	1. Confessions and Heart Break

Life has been pretty great for Peter Parker.

Sure, he rose from the dead three months ago, and it had been quite the transition after learning that he had been completely non-existent for five years, but he liked to think that he had done a good job at falling back into his old life. He and Tony Stark have been closer than ever, almost inseparable at times. He and Ned hang out just as much, if not more, doing all the nerdy stuff that Tony teases him playfully about whenever Ned decides to join him in his trips to the Stark Tower (Tony decided to build one closer to Peter, one with a giant room that Peter had all too himself). He started a healthy relationship with none other than MJ, who occasionally yells at him for coming home with a bullet wound or knife stuck in his side after patrol.

Yeah, Peter would say he was living the dream. Except for one thing: he wasn’t allowed to become an Avenger.

The whole team believed in him, and they all agreed that Spider-Man would be a great asset. Even Aunt May was for it, saying that her young nephew was growing up and that if this was what he wanted to do with his life, he should go for it (as long as he doesn’t skip college, of course). However, a certain billionaire refuses to let him join officially. Every time Peter brings it up to the elder man while they are working in his lab, watching a movie together, or even playing with Morgan, he always changes the subject. He constantly refuses to acknowledge the fact the Peter is a superhero, always keeping away from the topic of Spider-Man, Thanos, or anything related to Peter’s nightly activities.

Honestly, Peter was understanding for the first month. Superheroism was a touchy subject for everyone for a while, and he even took a break from being Spider-Man, trying to focus on just being a normal kid and trying to forget about the Decimation. But after a month went by, he decided to seek professional help, something that May had actually suggested multiple times. And after that, he found himself getting back into the flow of normality.

Tony Stark, however, refused to move on. He refused to sit down and talk about it, to put everything out on the table, to open up. He had locked all the doors to his feelings, barricading the entrances and putting up walls that Peter could every now and then squeeze through on a good day. But it would only last for two seconds before the walls were built up again.

Steve kept telling Peter to be patient, to wait for Tony to be ready. Everyone kept telling him that. But the seventeen-year-old is getting impatient with his mentor/father, to the point where he wants to punch a wall. He knew he was ready for more. He knew that he could help so many more people. But Tony, the man he trusted with his life, was holding him back.

“Penny for your thoughts?” 

Peter looked up from his math homework to see his girlfriend, her eyes not leaving the book she had laid across her lap. “I’m doing math equations,” he replied, confused.

She scoffed, turning the page, still not looking at him. How does she read and speak at the same time? Sometimes Peter wonders if MJ is really human. “You’ve been staring at the same problem for five minutes. I don’t think that derivatives are that difficult for the genius, dorky Peter Parker.”

“What? I haven’t-” Peter rolled his eyes playfully after a second. “I was just thinking.”

“I noticed, which is why I was asking about it.” When Peter didn’t say anything, she sighed and looked up, pulling a penny out of her pocket. “Are you going to make me actually pay you a penny for your thoughts?”

Ned, who had been watching the interaction while hunched over his history homework, chuckled. “Seriously, Dude. You keep staring into space.”

“I do not-” Peter cut himself off when his best friend and significant other gave him identical, over-exasperated looks. He sighed. “Mr. Stark still won’t let me be an Avenger.” MJ pursed her lips and Ned looked at him sympathetically. 

“Peter, Boss told me to remind you that his name is Tony, not Mr. Stark, and that I will have to play this message whenever you call him Mr. Stark and he’s not present,” FRIDAY’s voice sounded, echoing around the spacious living room. Peter groaned as Tony’s voice replaced FRIDAY’s, burying his face in his homework. He was singing a song about Spider-Man in the tune of the song Happy Birthday. And let’s just say it wasn’t about how heroic the Super Spider was. 

Both MJ and Ned were snickering when the song ended, and FRIDAY said, “Would you like me to replay the message?”

“No, FRI,” Peter said quickly, almost begging. “But do me a favor and tell Tony that I will not hesitate to hack into the tower and delete that message.”

“Yes, sir.”

“Dude, what even is your life?” Ned asked with a laugh. Peter only groaned in response.

*****

“I see that you got my message,” Tony said, not looking up from whatever he was tinkering with.

The moment Peter walked into the lab after Ned and MJ had left, he had let out a groan and slumped into his seat while muttering something that sounded like, “You’re the most insufferable man I know.”

“Oh, and good luck hacking the tower. I doubt you will get very far.”

“Whatever you say, Tony,” Peter replied, putting emphasis on the billionaire’s name. Tony only chuckled in response, which was followed by about an hour of silence, only interrupted by some random banter between the two of them, or asking the other to pass a certain tool. Ever since Peter had gotten back, their relationship consisted of science, tinkering, and sometimes movie nights that usually ended with Peter falling asleep on Tony, and the soft-hearted and loving billionaire carrying his son/protege to bed. In addition, the teen babysat Morgan sometimes. The two got along great, which made Tony much happier than Peter thought it would.

“You will not believe what happened on patrol the other day,” Peter said abruptly, speaking a little slower than he usually would, being cautious of his wording. Despite his carefulness, Tony tensed slightly at the mention of Spider-Man. For the last week or two, Peter was slowly bringing up Spider-Man every now and then, trying to ease Tony slowly back into reality. “This guy tried to rob a freaking bank by shooting a window,” he continued with a chuckle, rolling his eyes at the criminal’s stupidity.

This was the first time Peter had brought a weapon into his small mentions of his superheroing, and he didn’t miss how Tony’s hand shook a little. But him being the stubborn Spider he was, he kept going. He was getting impatient, and he didn’t understand why Tony was still so upset. He knew he could talk to him. Peter was always open to talk to, to confide in. But the billionaire was just as stubborn, if not more, than the teen.

“The alarms went off, naturally, so I probably could have just left him there. But then he kind of saw me and threatened to shoot, but his hand was shaking so much that I doubt he would have been able to anyway-” Peter was cut off when Tony dropped his mug, coffee and glass shards going flying, staining the ground brown. “Tony…?”

Said man was shaking, gripping the table tightly, knuckles white. His breath was shallow, and he was panting, eyes screwed shut. Peter, unsure of what to do, placed a hand on Tony’s shoulder, earning a whimper from the man. Seconds later, Peter found himself trapped in his mentor’s arms, who was clinging to him as if his life depended on it, as if Peter might disappear if he let go.

Peter immediately felt guilty. He shouldn’t have gone so far. He knew Tony didn’t like the subject of Spider-Man, although he didn’t know why, and it was his fault that the man was in this state. Slowly and carefully, Peter led him to the couch, avoiding glass shards along the way. When they were seated on the leather couch, Peter instructed Tony, who was still clinging to him, to match his breathing. And after a couple of minutes of deep breaths and frantic hugging, the billionaire was calm again.

“Spider-Man was a mistake,” was the first thing out of Tony’s mouth. Peter froze. What?

“What?” the teen asked, voicing his thoughts.

“I made you think you were ready, led you to believe that you were capable of being a superhero, but you can’t- you’re not-”

“I-I don’t understand,” Peter said, his voice shaking a little. “You don’t think I’m good enough?”

Tony sighed, running a hand over his eyes. “Peter, you died. And it was my fault. I shouldn’t have let you be Spider-Man. I should have made you go to school, pay more attention to college… but I guess it’s too late to stop you.”

“B-but Mr. Star- Tony, I’m fine now. And I am more than ready for more. I’m capable of fighting harder fights, protecting the world, and everyone else agrees with me about being an Avenger-”

“No,” Tony’s voice cut through the teen’s hopeful words, killing it with a single word. “You will not be an Avenger. Not now, not ever. You can’t.”

Those words cut deep. Each syllable was equal to a sharp knife digging into his heart, crushing it, and throwing it out the window. He just stared at his mentor in shock, who wasn’t looking at him. And after the shock wore off, it was replaced by anger and the heavy, hot feeling of betrayal being forced upon his trembling shoulders. The man he had looked up to his whole life didn’t believe in him and claimed that believing in him at all was a mistake. 

And the first words that Peter’s confused, muddled, and angered mind could think of were, “I hate you.” And before he could see the look of hurt, shock, and shame cross the billionaire’s face, he ran out the door.


	2. A Proposal

_ The air was hot, dry, and tasteless. Dirt and dust lingered around them, making the oxygen more toxic than beneficial, and causing many of the supposedly unstoppable heroes to cough and distract them from their mission. However, in this minute, the mission was going terribly wrong, for half of the dust in the air wasn’t from the planet, but the heroes themselves. One by one, heroes dropped like flys, their remains going to the heavens. _

 

_ “Mr. Stark?” _

 

_ No. _

 

_ “I don’t feel so good.” _

 

_ “You’re fine,” was Tony’s response, his voice coming out as cracked and hoarse. He was lying. The young teen wasn’t alright. Nothing was alright right now. _

 

_ “I-I don’t know what’s happening- I-” the words barely left the teen’s mouth before his weight was suddenly thrust upon Tony. And having been unprepared for him, Tony lowered Peter to the ground as gently as possible, frantic eyes searching his kid over for any signs of normality.  _

 

_ Please be okay. _

 

_ Please be okay. _

 

_ Please be okay. _

 

_ “I don’t wanna go,” Peter’s broken voice washed over the man of steel, causing his heart to clench and bleed with grief and guilt. Why his kid? _

 

_ Why, God, why? _

 

_ “Please, sir, I don’t wanna go,” the incredibly small looking teen whimpered, and Tony wanted nothing more than to hug the boy to his chest, to shield him from the reality of the situation, to promise that he won’t let him leave.  _

 

_ But his mouth remained closed. He didn’t move.  _

 

_ Peter started to disappear, his body turning to dust, starting at his feet and spreading to his chest and up to his neck. And before he was gone, he looked straight into Tony’s eyes and said, “You could have saved me. This is your fault.” _

 

_ Your fault. _

 

_ Your fault. _

 

_ Your fault. _

 

_ He wouldn’t have died. _

 

_ It’s all your fault. _

 

_ Tony Stark, the great Iron man, couldn’t even save his own child. _

 

**_It’s your fault._ **

  
  


The cold and fuzzy carpet was the first thing Tony Stark was aware of. Next, he could feel the warm and sticky sheets wrapped around his legs. And finally, his eyes opened to reveal his dark room, shadows lingering in the corner and creating shapes and images he didn’t want to see.

 

“Tony?” he groggy, yet concerned voice came from above him.

 

He took a breath, his hands shaking as he ran a hand through his hair, sweat making him feel sticky and shivery. “I-I’m fine, Pep. I just fell off the bed.”

 

The sound of shuffling was all he heard before Pepper’s face appeared, looking over the edge of her bed and down at her husband. After a long moment of her having a staring contest with him and him trying to hide the waterfall of emotions fighting to be released, she finally said, “You had another nightmare.”

 

Tony winced at the word. Ever since he was a teen, the very word nightmare made him shiver. He hated it. Why did the damn thing exist, anyway? What was the point? To haunt you? In fact, dreams, in general, shouldn’t be a thing. Everyone would have much easier and happier lives if they didn’t have to deal with reliving embarrassing, terrifying, or traumatizing situations.

 

“Would you believe me if I said no?” he asked quietly, quickly pulling himself back into the bed and laying down next to his wife, who reached up and played with his hair. He relaxed.

 

“No. Not at all,” she responded, a bittersweet smile tugging at her lips.

 

He sighed overdramatically, giving her a quick peck on those oh so tempting lips. “It’s scary how well you know me.”

 

“Well, I did babysit you for over a decade,” she replied easily, her eyes glinting.

 

He smiled a little. “And for that, I am in your debt.”

 

“Which you can pay off by telling me what’s going on.” After a moment of silence, she added, “Is it Peter?”

 

He tensed before pulling her close and burying his face in her hair, breathing in the smell of her conditioner. “Maybe. And it might be of him dying on that damned planet. And he might also be blaming me for his death in the dream, which may or may not be tearing me apart,” he said casually, almost as if he was talking about what type of coffee he preferred.

 

She hummed a little, her hands still doing wonders as they ran through his curls. “That’s not all that’s bothering you.”

 

Tony sucked in a breath, his body tensing. “I… well, we got in an argument earlier, and I- well, I guess I- I don’t know-”

 

“You’re afraid that you lost him emotionally,” she finished for him without missing a beat.

 

“Yeah,” he breathed out, his arms locked tightly around her. “He said that he hates me.” The hurt and fear could be easily heard in his voice as the words escaped his mouth.

 

“He doesn’t,” Pepper told him calmly, one of her hands rubbing his back now. “Just give him a chance to calm down, and…” she hesitated before continuing, “and maybe you should listen to him.”

 

Tony pulled away from her, his expression accusing. “Don’t tell me you’re taking his side. He’s not becoming an Avenger!”

 

“Tony-”

 

“I’m going to the lab,” he interrupted, a mixture of anger and bitterness in his voice, his hands shaking. “Sorry for waking you up.” Before Pepper could protest, he had left the bedroom, no doubt about to kill himself with sleep deprivation and coffee.

 

Pepper sighed. Sometimes she thought she was raising two kids.

 

*****

 

**Uknown Number:** _Meet me at the Waffle House two blocks away from your current location._

 

Peter had gone straight to Ned’s house after leaving the Stark Tower. He was going to spend the night with Tony, but after what happened, he had no interest in being anywhere near that man. He was angry, betrayed, but most of all hurt. Tony was almost like a father. Heck, any strangers who saw them interacting assumed that they were related.

 

And it hurt like hell when his supposed father said that believing in him was a mistake. 

 

And staring down at this text at three in the morning, he honestly didn’t feel like getting kidnapped or meeting some pervert at Waffle House, of all places. However, part of him wondered if it was Tony. He had deleted his mentor’s number from his phone out of anger and resentment, and he hadn’t bothered to memorize his number before doing it. As of right now, he had no interest in contacting the billionaire.

 

Although, his naturally optimistic self convinced the angry part of him that Tony wanted to apologize, which was why he wanted to meet. That would explain why it was at such a ridiculous time. Tony didn’t seem to know what sleep was.

 

Stepping over Ned, who had fallen asleep with a bowl of spilled popcorn, which was all over the floor, gripped in his arms like a teddy bear, he pulled on his suit and pulled a coat on over it before jumping out the window. Once he was outside the Waffle House, he pulled his mask off and stuffed it in his jacket pocket, zipping up the jacket itself to hide his suit. 

 

He had never been to Waffle House at 3:00 am, but it was as bad as he expected it to be. There was a drunk couple making out in the corner, not bothering to be very quiet, while multiple drunk and high people were sitting around eating or just trying to keep themselves awake long enough to order. Grimacing, Peter looked around the small restaurant, hoping to see an out of place billionaire leaning against the wall or sitting at a booth.

 

“Mr. Parker,” a voice greeted from beside him. Peter jumped, turning to see a man sitting in the booth to his left. His jaw dropped.

 

“N-Nick Fury?” he asked, the sound of disbelief rolling off his tongue easily. “Are you really…?”

 

Nick raised his eyebrows and said, “How many other black men with an eye patch do you know?”

 

Despite the fact that he knew it was rhetorical, Peter felt as if he was supposed to answer. “I- um- none. I think.”

 

Nick motioned for Peter to sit down, and the teen quickly complied, his eyes wide as saucers. “Do you know why I’m here?” Nick asked.

 

“I, uh, no, sir. Am I supposed to?”

 

“No,” he answered tersely, his one eye trailing on a man who had just walked in. Peter squirmed in his seat, unsure of what to say or do. For a couple of minutes, they sat in silence, and Nick Fury just stared at him, his gaze calculating. Abruptly, he asked, “What do you know about Hydra?”

 

Surprised, Peter stumbled over his words, saying, “N-not much, sir. I, um, it was a dangerous group that Captain America had to fight…”

 

Nick sighed, seemingly disappointed with Peter’s lack of knowledge on the subject. “It’s a terrorist group, one that we keep thinking is gone, but keeps popping up on our radar and catching our attention. They refuse to disappear.”

 

“Our?”

 

“S.H.I.E.L.D.’s.”

 

“I thought S.H.I.E.L.D. was-”

 

“Disbanded? It was. But there are some agents who are still working with me, and we like to identify ourselves as S.H.I.E.L.D.,” he explained. “Recently, we caught sight of some Hydra activity. We don’t know what they’re up to this time, but I don’t think it’s good.”

 

Peter fought the urge to scoff at his words. Of course it wasn’t good. This was a terrorist group they were talking about. “With all due respect, sir, why are you telling me this? At 3:00 am?”

 

The edge of Nick’s mouth twitched, almost like he was trying not to smile. “I need your help.”

 

His words hung over the table, thick and heavy like a raincloud waiting to burst. Nick Fury, of all people, needed his help? Millions of questions bubbled up all at once, but he pushed them down, deciding that only one was important. “Why me? Wouldn’t the Avengers be more qualified? They’ve dealt with this before.” He bit down the bitter taste in his mouth. He would be one of the Avengers and be qualified for this if it weren’t for Tony.

 

“Yes, but they tend to make more… noise,” he said slowly. “We need someone sneaky who can get in and out without them knowing we were there in the first place.”

 

Peter couldn’t help but smirk. “You need someone who can climb on walls and is small.”

 

Nick’s eyes glinted with amusement. “Precisely.”

 

After a moment of silence, during which they had a mini staring contest, Peter decided that this was exactly what he needed. If he could handle this, Tony would have no choice but to accept him into the team. With a grin, Peter said, “Just tell me what you need me to do.”

**Notes for the Chapter:**

> I know I should have waited to post this, but I'm just too impatient. I hope you liked it!

**Author's Note:**

> Oof, Tony REALLY messed up this time.  
> I hope you guys liked it, and I will be posting another chapter soon!


End file.
